State of the art computational thechniques were applied to several current research toppics in biocatalysis such as substrate promiscuity, reaction promiscuity and high throughput mutant generation and screening. The studied subjects are of great interest to industrial biocatalysis nowadays and can find large application for rational redesign of inefficient biocatalysts and fast substrate engineering and screening. The overall work can be devided into three principal areas, i.e. understanding catalytic mechanisms, description of enzyme-substrate interactions and integration of available computational methods for the development of a novel authomatized tool for enzyme engineering. In each of these areas, the goal has been to test the existing methodologies as well as the development of new descriptors and ready to use strategies.